Imaging Platform

Reproducible image-based profiling with Pycytominer.

Serrano E, Chandrasekaran SN, Bunten D, et al. Reproducible image-based profiling with Pycytominer. Nature methods. 2025. doi:10.1038/s41592-025-02611-8DOI Google Scholar PubMed

Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes.

Ewald JD, Titterton KL, Bäuerle A, et al. Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.01.22.634152DOI Google Scholar PubMed

Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.

Riendeau JM, Gillette AA, Guzman EC, et al. Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images. Scientific reports. 2025;15(1):5548. doi:10.1038/s41598-024-82639-6DOI Google Scholar PubMed

A genome-wide atlas of human cell morphology.

Ramezani M, Weisbart E, Bauman J, et al. A genome-wide atlas of human cell morphology. Nature methods. 2025. doi:10.1038/s41592-024-02537-7DOI Google Scholar PubMed

From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability.

Seal S, Carreras-Puigvert J, Singh S, Carpenter AE, Spjuth O, Bender A. From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability. Molecular biology of the cell. 2024:mbcE23080298. doi:10.1091/mbc.E23-08-0298DOI Google Scholar PubMed

Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes,

García-Ortegón M, Seal S, Singh S, Bender A, Bacallado S. Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes,. In: 2024 Workshop on Data-Centric Machine Learning Research, International Conference of Machine Learning. bioRxiv; 2024. doi:10.1101/2024.06.07.598036DOI Google Scholar

Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions.

Cimini BA. Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy. 2024. doi:10.1111/jmi.13288DOI Google Scholar PubMed

Cell Painting: a decade of discovery and innovation in cellular imaging.

Seal S, Trapotsi MA, Spjuth O, et al. Cell Painting: a decade of discovery and innovation in cellular imaging. Nature methods. 2024. doi:10.1038/s41592-024-02528-8DOI Google Scholar PubMed

Building momentum through networks: Bioimaging across the Americas.

De Niz M, García RE, Ramirez CT, et al. Building momentum through networks: Bioimaging across the Americas. Journal of microscopy. 2024. doi:10.1111/jmi.13318DOI Google Scholar PubMed

Reproducible image-based profiling with Pycytominer.

Serrano E, Chandrasekaran SN, Bunten D, et al. Reproducible image-based profiling with Pycytominer. ArXiv. 2024.Google Scholar PubMed